phylo4com: Create community phylogenies object
In ecoPD: Ecologically-informed phylodiversity metrics

Description Usage Arguments Details Value Methods Author(s) See Also Examples

Function to combine species abundance data with phylogenetic information for a set of communities.

  ## S4 method for signature 'phylo4,numeric'
phylo4com(x, n, communityID, species,
    missing=c("warn", "OK", "fail"))
  ## S4 method for signature 'phylo4,matrix'
phylo4com(x, n, missing=c("warn", "OK", "fail"))
  ## S4 method for signature 'phylo4,data.frame'
phylo4com(x, n, missing=c("warn", "OK", "fail"))
  ## S4 method for signature 'phylo4d,missing'
phylo4com(x, n, cols)
  ## S4 method for signature 'phylo,ANY'
phylo4com(x, n, ..., check.node.labels = "keep")

`x`	a phylogeny of class `phylo4d`, `phylo4`, or `phylo`
`n`	Vector of abundances of each species in each community, or abundance matrix with species as rows and sites as columns.
`communityID`	Vector of community labels corresponding to the abundance values (only used if `n` is a vector).
`species`	Vector of species labels corresponding to the abundance values (only used if `n` is a vector).
`cols`	Names of pre-existing phylo4d data columns to use as abundance data (only if `n` is missing)
`check.node.labels`	If x is a phylo object, what to do with node labels
`missing`	(not currently implemented) What to do if some requested node IDs or names are not in the tree: warn, do nothing, or stop with an error.
`...`	additional arguments to be passed to other methods

TODO

If the species vector contains values that do not appear in the tree, they are ignored with a warning. If a community has fewer than one species matched in the tree, an error will result. In both cases, the behavior is simply a result of how the phylobase subset method works; see the help page for this method for more information.

A phylo4com objects.

x = "phylo4", n = "numeric": creates community phylogenies from a master phylo4 tree, a vector of abundances, a vector of corresponding community names/labels, and a vector of corresponding taxa names/labels
x = "phylo4", n = "matrix": creates community phylogenies from a master phylo4 tree and a site-by-species abundance matrix.
x = "phylo4", n = "data.frame": creates community phylogenies from a master phylo4 tree and a site-by-species abundance data.frame
x = "phylo", n = "ANY": creates a phylobase tree from an object of class phylo

Jim Regetz (regetz@nceas.ucsb.edu)

subset in the phylobase package

  # Example of phylo4com construction
  data(weeds.data)
  data(weeds.tree)
  phylo4com(weeds.tree, weeds.data$cover, weeds.data$plot,
    weeds.data$taxa)